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- PDB-3ak9: Crystal structure of the SEp22 dodecamer, a Dps-like protein from... -

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Basic information

Entry
Database: PDB / ID: 3ak9
TitleCrystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis, FE-soaked form
ComponentsDNA protection during starvation protein
KeywordsMETAL BINDING PROTEIN / Oxidoreductase / Dps-like protein / dodecamer / Iron-binding protein
Function / homologyFerritin, core subunit, four-helix bundle / Ferritin / Up-down Bundle / Mainly Alpha / : / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Kentucky (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMiyamoto, T. / Asahina, Y. / Miyazaki, S. / Shimizu, H. / Ohto, U. / Noguchi, S. / Satow, Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structures of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis
Authors: Miyamoto, T. / Asahina, Y. / Miyazaki, S. / Shimizu, H. / Ohto, U. / Noguchi, S. / Satow, Y.
History
DepositionJul 8, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
G: DNA protection during starvation protein
H: DNA protection during starvation protein
I: DNA protection during starvation protein
J: DNA protection during starvation protein
K: DNA protection during starvation protein
L: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,25134
Polymers224,90712
Non-polymers1,34422
Water23,7981321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44550 Å2
ΔGint-135 kcal/mol
Surface area56260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.471, 98.003, 208.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DNA protection during starvation protein / SEp22 / Dps-like protein


Mass: 18742.254 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Kentucky (bacteria)
Strain: CVM29188 / Plasmid: pMAL-p2X / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: B3YEF4, Oxidoreductases; Oxidizing metal ions
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1321 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: Reservoir solution: 0.1M sodium acetate, 0.3M magnesium chloride, 28% PEG 400. The crystal was soaked in the solution containing 0.1M MES pH6.0, 0.25M magnesium chloride, 30% PEG 400, 0.1M ...Details: Reservoir solution: 0.1M sodium acetate, 0.3M magnesium chloride, 28% PEG 400. The crystal was soaked in the solution containing 0.1M MES pH6.0, 0.25M magnesium chloride, 30% PEG 400, 0.1M ascorbic acid, and 0.1M ferrous ammonium sulfate., pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2009
RadiationMonochromator: TRIANGULAR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→48.6 Å / Num. all: 448407 / Num. obs: 407378 / % possible obs: 90.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.8
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.4 / Num. unique all: 31051 / % possible all: 89.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AK8

3ak8


Resolution: 1.3→48.6 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.455 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 21511 5 %RANDOM
Rwork0.1526 ---
all0.1536 407378 --
obs0.1536 407378 90.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.381 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.3→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14764 0 46 1321 16131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02215103
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.94720503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.57851885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04324.914755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.715152687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4681596
X-RAY DIFFRACTIONr_chiral_restr0.0840.22400
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211348
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.59304
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.026215028
X-RAY DIFFRACTIONr_scbond_it3.16535799
X-RAY DIFFRACTIONr_scangle_it4.6434.55456
X-RAY DIFFRACTIONr_rigid_bond_restr1.382315103
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.299→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 1510 -
Rwork0.196 29541 -
obs-31051 89.44 %

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